


The Way Home

by Tarlan



Category: Stargate Atlantis
Genre: Angst, Community: sgareversebang, M/M
Language: English
Status: Completed
Published: 2014-05-19
Updated: 2014-05-19
Packaged: 2018-01-24 06:47:58
Rating: Explicit
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 10,535
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1595516
Author URL: https://archiveofourown.org/users/Tarlan/pseuds/Tarlan
Summary: <blockquote class="userstuff">
              <p>The opportunity to study Atlantis while she rests on Earth seems too great for the I.O.A. to resist, but as far as John is concerned, Atlantis belongs in Pegasus, and Rodney belongs on Atlantis... and if John could have his dreams come true, then Rodney would also belong with him.</p>
            </blockquote>





	The Way Home

**Author's Note:**

  * For [Syble](https://archiveofourown.org/users/Syble/gifts).
  * Inspired by [Where's John?](https://archiveofourown.org/works/1629110) by [Syble](https://archiveofourown.org/users/Syble/pseuds/Syble). 



> Written for SGAReverseBang for Syble4's amazing art piece, Where's John?

John looked out across the beautiful, calm blue ocean towards the Golden Gate Bridge and the distant shoreline of San Francisco. Although he had grown up on his father's ranch, surrounded by green fields that he rode almost daily on his favorite of his dad's horses, he had spent many summers on the Californian coast with his maternal grandparents. They'd had a modest house fronting onto the beach and he had spent his days surfing and skateboarding with Dave. They were good memories, full of laughter and sunshine, and when he thought of his mother it was the memory of her settled on a beach towel under a parasol, smiling and waving back when he called for her attention from the surf's edge.

'Watch me, mom! Watch me!'

He smiled at the memory, looking along the balcony to share this moment with Rodney only to feel his happiness bleed away as Rodney placed an arm around Keller and drew her close.

It shouldn't hurt so much but all the promises he had made to himself after losing Holland had crashed around him after he met Rodney. Holland had been so much more than a friend, and if the military court had known about the clandestine relationship he'd had with Holland then ' _disobeying a direct order_ ' would have been the least of his concerns. Fortunately for John, the court had focused on him disobeying orders and had not looked deeper into the reason why he had risked so much for one man. His defense had played the mild PTSD card, citing that he had lost two of his best friends in an attack only days earlier, and that was probably the only reason why they had transferred him to Antarctica with a black mark on his permanent record rather than give him a dishonorable discharge.

After the court martial he had sworn never again to get too emotionally involved with another person, especially another guy, though he had amended that to not getting involved while he was still serving in the military. Then he had met Dr. M. Rodney McKay, PhD, PhD, and John had fallen instantly in lust for the bright, excited grin and the sparkling blue eyes.

The broad shoulders and fine ass hadn't hurt either.

Over the past years he had done everything in his power to make sure his friendship with Rodney remained platonic. He had pushed Rodney away whenever it looked as if they were getting too close, and he had tried to be supportive whenever Rodney developed a crush on someone else. Except that wasn't strictly true, he thought wryly, but fortunately only Teyla and Ronon had picked up on how often John sabotaged Rodney's relationships, unintentionally for the most part.

The quarantine lock down that had seen the end of Rodney's relationship with Katie Brown had been John's fault, though he had never admitted that out loud to anyone - not even to Teyla though he suspected she knew but had said nothing. His high anxiety over Rodney's imminent plans to propose to Katie had heightened after Teyla entered the laboratory to speak with Rodney, just as Rodney was rushing off to ' _go get the girl_ ' with John's ' _blessing_ '. Teyla had raised a single, admonishing eyebrow at John, and John could recall wishing fervently that all the doors int he city would seal to prevent Rodney reaching Katie and asking for her hand in marriage.

For once, Atlantis had picked up on his thoughts and she had interpreted it as a mental command, issuing the quarantine lock down.

No doubt Teyla and Ronon could name other occasions where John's subconscious actions or inaction had sent yet another potential love match for Rodney walking away alone, with Rodney none the wiser, but John had to admit that he had few regrets over Katie. She had been all wrong for Rodney, and though the lock down had backfired in some ways by locking Rodney and Katie in the same room together, it had put Rodney under enough stress for him to drop the ' _nice_ ' facade he wore around Katie and be himself in all his acidic and blustering glory.

Katie hadn't liked this real Rodney and she had broken off their relationship.

Keller, on the other hand, had seen Rodney at his worst and that had not discouraged her. Perhaps she thought she could mold him into being the nicer person he had become while losing himself to that alien parasite in his brain, but then he wouldn't be John's Rodney anymore. John liked the acerbic, sharp-tongued, quick-minded and irascible Rodney McKay that snapped and snarled even as he saved their collective asses from the latest threat of annihilation.

What John hadn't anticipated was Keller not only being undeterred by Rodney's less than stellar traits but choosing Rodney over Ronon.

He still kind of felt a little bad about silently routing for Ronon because it was for all the wrong reasons. Ronon was his friend too and he deserved better from John, but John's emotions had been conflicted. On the one hand he wanted both of his friends to be happy, and on the other, he wanted to be happy too. Except John knew he rarely got what he truly wanted, often refusing to snatch at a chance for happiness because, in his eyes, others deserved it more.

Woolsey was the first to step back from the rail and head back inside and though it was warm on the balcony, the cool breeze coming off the sea gave Carson enough cause for concern that he ordered Ronon back to the infirmary. This left just four of them, and John looked away from the contented couple, a knife twisting inside as he heard Keller laugh at something Rodney said to her, their words caught on the soft breeze and snatched away. As he turned to walk away, the knife twisted again when he heard Rodney laugh in response, and his steps faltered, but Teyla's small hand on his arm drew him onwards, leaving Rodney and Keller alone on the balcony.

She walked beside him as he followed Ronon, Amelia and Carson, her voice low and sincere.

"You must speak with him soon or risk losing him forever."

John glanced at her, ready to pretend he didn't understand what she was talking about but the hard glint of warning in her eyes made him sigh and remain silent. She was right, but that didn't change anything because he had already convinced himself that he was staying silent for Rodney's sake rather than for his own. Rodney deserved to find happiness. He deserved a chance to have a normal life with a wife and kids, and even a white picket fence if that was what he wanted. Perhaps Teyla was right and he would lose Rodney to Keller if he stayed silent, but at least they would still be friends.

That was when John realized that his feelings for Rodney ran far deeper than he'd allowed himself to believe, and the shock of that inner revelation must have shown on his face.

"John?" Teyla stopped him, and he stared down into her concerned face for a moment before shoving everything back behind his usual laconic smile, deliberately easing the tension from his body, and giving her a one shouldered shrug.

"Have you ever been surfing?"

"Surfing?"

"Ronon will love it. You both will love it," he stated emphatically, and Teyla gave a half-hearted smile as they carried on walking.

***

The next few weeks were filled with more activity than John could recall since those frantic days in the first year, when they prepared for the arrival of the Wraith. He was surrounded by unfamiliar faces. Some had come to assess the status of the city, with engineers working under Radek and Rodney's guidance were repairing damaged sections, and the military contingent had quadrupled with dozens of teams set up to explore the city. Yet with all the new manpower, John knew it could still take months, perhaps years to explore every part of a city the size of Manhattan. Even then they could still miss a hidden room or closet, just as they had not known of Janus's secret laboratory until Daniel Jackson learned of its possible location from reading the logs and diaries from Janus's peers, lovers and assistants.

In addition to military, scientists from all disciplines had poured into the city, each looking for answers and new discoveries in their respective fields now they didn't have to risk being eaten by a Wraith or cut off from Earth indefinitely. Yes, he realized that was a little mean of him to think of them that way but Rodney had ranted about it only the other day. At the time John knew it was more likely that Rodney simply wanted to be at the forefront of all discoveries in the city, and he smiled in remembrance as he thought back to that rant.

"Admit it, Rodney, you're just worried someone is going to discover a hidden cache of ZPMs... and take all the glory."

"What? No! Of course I'm not..." Rodney slumped onto the bed next to John with a heavy sigh. "Oh, who am I trying to kid. Yes. I'll admit that thought had crossed my mind. I can be a... petty man on occasion."

John raised an eyebrow.

"Fine, I can be petty most of the time, but that's my third biggest fantasy after winning the Nobel for my astounding and world changing body of work. The Wormhole Drive alone could revolutionize space travel-."

"What's the first?"

"What?"

"You said finding a cache of ZPMs is _third_ to winning a Nobel, so what comes first?"

Rodney's face heated in embarrassment, and he spluttered as John's question effectively derailed him from the rest of his tirade about _Fair Weather scientists_ who wouldn't put their lives on the line when Atlantis was facing the Wraith but were now trampling all over _his_ city.

"I meant second, not third."

"No you didn't," John stated nonchalantly, picking up a cloth to finish cleaning his skateboard, and almost enjoying the way Rodney began to squirm and fluster even as he prepared to hear something that might break his heart. John could imagine that big brain running through dozens of different rebuttals right now, or desperately trying to think up something that could be more important to Rodney than ZPMs and Nobel awards.

Rodney snapped his fingers.

"Fine. Sam Carter. Naked."

John frowned, hand pausing mid-stroke along the length of the skateboard's surface. He could tell that was a lie even without looking for the tell-tale twitches that Rodney could never hide, and which made him the perfect poker opponent as it meant John always cleared the table. Rodney's crush on Sam had diminished after she took over Atlantis following the loss of Elizabeth, especially as Rodney was already in a steady relationship with Katie by then. By the time that had fizzled out and Katie had returned to Earth, Keller had started making overtures of friendship with Rodney and Rodney's crush on Sam had turned to one of respect for her as a scientist, a leader, and a friend.

Before John could say anything, Rodney jumped to his feet and rubbed his hands together nervously.

"No time left for idle chitchat. I have very important work to do."

John's thoughts came back to the present as he recalled how Rodney had left as if the hounds of hell were nipping at his heels, leaving him sitting on the bed feeling puzzled by Rodney's strange behavior. Rodney had been avoiding him since then so John was no closer to figuring out just what the hell had happened, but he had noticed a slight chill between Rodney and Keller too. Fortunately, Rodney couldn't avoid him any longer as they were scheduled for an exploration today.

He glanced across to where Teyla was adjusting her TAC vest, slipping items into the pockets in readiness. Beside her, Ronon was inspecting his blaster even though John really didn't expect him to need it, but he wasn't going to argue. On the other side of the Gate Room, he could see Rodney's hands flailing as he argued with Radek over the priority of some of the repairs. He was too far away to hear every word but he had to hide a smile when Radek threw his hands in his air and walked away.

"Sir, Team Four are ready to move out."

John nodded as Captain O'Donald headed for the transporter with his team following on behind. He was still surprised that O'Neill had not reassigned him as soon as Atlantis reached Earth, having half expected someone of higher rank like Caldwell or Ellis, or even a one-star General to jump at the chance of taking military command of Atlantis. Lorne was still his 2IC, but he had set out earlier with his team and some additional botanists to explore a building that had once housed Botany and Agriculture laboratories.

Team Four would be taking a closer look at a structure near the East pier while John's team and a cultural expert, Doctor Tina Martinis, would explore the taller building next to it. According to the Ancient database, the smaller structure had housed some of the Ancient refugees who had fled to Atlantis from other planets in Pegasus as the Wraith slowly took over the dwarf galaxy. The building next to it had supposedly housed a cultural museum and library as well as several floors containing the private offices and homes of some of the city's higher administrators. In particular, those of two Ancients who had gained mythical fame or notoriety on Earth - Counselor Ganos Lal, who had taken the name of Morgan le Fay, and High Counselor Moros, who was better known in Earth mythology as Myrddin - Merlin.

"McKay!" John called out before Rodney could stomp off after Radek. "Get your ass over here."

***

The lower floors had seen minor damage from where a Wraith dart was brought down during the siege that first year but, structurally, the tower was still sound so they moved into the building. The ground floor was open-planned with pedestals standing at random intervals throughout.

"Huh!"

John was about to ask Rodney what had caught his attention but then he spotted it. The pedestals were not random at all but were grouped, following Fibonacci's mathematical formula that had them spiraling out from the center of each section. Then he noticed that the stained glass windows were fitted with moving mirrors so a beam of natural light would illuminate each pedestal throughout the day. The pedestals themselves were standing empty, with their treasured artifacts long since removed either into storage or perhaps sent to Earth when the Ancients abandoned Atlantis.

Doctor Martinis walked to the center of the floor and turned in a circle, and John smiled at her awed expression. She was one of the scientists that hadn't risked joining the expedition while Atlantis was in Pegasus but, in her case, he could understand her reluctance. Although she moved well, her medical file stated that she suffered from severe arthritis, requiring several joint replacements before she was even out of her teens. Eventually, the advancements found on Atlantis would be released into the medical community on Earth, easing the suffering of millions like her.

Nanotechnology was a small part of that, and John felt a wry smile twist at his lips at the unintended pun as he recalled how pushing too fast with their discoveries on Atlantis could be equally dangerous. Jeannie Miller had almost become a victim of nanotechnology gone mad due to a father's desperation to save his dying daughter.

John shuddered because Jeannie was not the only person he cared about that he had almost lost that day. Rodney had offered to be fed on by a dying, starved Wraith - by Todd - because Todd was the only one able to help Jeannie in time. Convincing Henry Wallace to take Rodney's place still preyed on John's mind even after all this time. He had taken a grieving father in an unstable, vulnerable state, and had convinced him to sacrifice himself to save Rodney's sister. He had justified it at the time as Wallace paying for his actions, and no one had questioned him beyond a short debriefing following the incident, but there were nights when he lay awake wondering if he was just as much of a monster as the Wraith. Each time, his fears were dispelled as soon as he saw Rodney, watching those clever hands flying as he excitedly explained a theory or angrily berated some underling who had screwed up... or simply just watching those fingers dancing over a keyboard or datapad. So alive.

They checked the whole floor but found nothing of interest beyond the Ancients' love of mathematics.

"Let's move on up," John ordered, hoping they would eventually find something that the Ancients had either overlooked or deemed too insignificant to remove.

The next two floors were as empty as the first but the one above that was different. The room was split down the center by a wall of mostly Ancient stained glass in gold and orange. It was still partially filled with pieces of pottery on display, sealed within static shields that had to be powered from something other than the main ZPM. Doctor Martinis almost squealed in delight, and John couldn't hold back a grin at Rodney's eye roll of disdain, aware of Rodney's grumble about soft scientists. 

Martinis began to visually examine each piece in turn, taking video footage and numerous photographs while making an audio commentary. She knew they couldn't spend long on each floor - just enough time to document and decide if the find required a more thorough examination at a later date.

While she worked, quickly and methodically, John and the rest of his team moved through the wide doorway that led to the other half of the floor. It was an open area with a transparent wall stretching almost from floor to ceiling along the entire length of the building, and along both ends, broken up only occasionally by support pillars. Beyond the window, the towers and spires of Atlantis stretched majestically into the cloudy blue skies of Earth. The only furniture was a single low bench seat that was slightly molded to allow nine people to sit; four each side and one on the far end. John decided it was placed there simply for the breathtaking view of the architecture surrounding this tower, and the sea and sky beyond. Judging from what he knew of the Ancients, it made more sense than anything else, and he wondered how often the Ancients would come here simply to sit and contemplate the world around them.

They moved to the window-wall and John looked down. The pier where the _Daedalus_ tended to land stood empty as the city was floating too close to the Californian coast to risk the _Daedalus_ being spotted descending through the atmosphere. Most of Earth still remained in blissful ignorance of the Stargate program and the threats that had come from beyond their little corner of the galaxy. There were times when he envied them, recalling the peace and clarity he had found during those months stationed in Antarctica.

"...And this probably doubled as a reception room," Rodney was saying.

"I do not understand why you believe there may be a separate power source." Teyla frowned, obviously at something Rodney had suggested, which John must have missed.

"When we fled Lantea during the Asuran attack, the shield contracted to encompass only the immediate area surrounding the central spire. All of that," Rodney huffed, expanding his arms to encompass the contents of the other half of the room, "would have been in zero gravity."

John finished for him, "So if the shields were not an independent source, then all of that would be broken pottery scattered across the floor."

Rodney clicked his fingers and pointed at him. "Exactly. And if we can find this power source, it might hold answers to producing better generators until we do find that cache of ZPMs, or a factory for making them." Rodney sent a crooked smile towards John, acknowledging at least part of their discussion from the other evening.

"Perhaps then Atlantis will have the power it needs to fly back to Pegasus," Teyla added.

Rodney waved a hand airily, without thinking as he replied, "Oh, there's more than enough power left in the ZPM to get us back home."

John hadn't really noticed how uptight Teyla and Ronon had been until this moment when he saw some of the tension roll off both of them. Teyla's gentle curve of lips became a rare smile that added sparkle to her eyes. Ronon gave a toothy grin too, leaning against one of the empty, waist height pedestals.

"So when do we head back?" Ronon asked, looking between John and Rodney for an answer.

John gave Rodney a hard glance before shrugging, seeing the guilt rising in a too expressive face; he pulled Teyla and Ronon's attention towards him instead.

"No idea. Woolsey has been going to these meetings with the I.O.A. but they're all pretty excited at having Atlantis on their doorstep. They want to spend a little time checking her out."

"And there are still repairs ongoing," Rodney added too quickly and nervously, "From the attack on the Superhive."

"I see," Teyla replied but some of the happiness had dimmed from her eyes. "Perhaps I should have accompanied Richard to these meetings, to ensure that all views concerning the future of Atlantis were taken into account."

"Yeah, probably."

John saw Teyla frown a little at his response and he wished he could tell her that the _talks_ had not been going that well at all - for Pegasus. It was inevitable that once the I.O.A. got hold of Atlantis on Earth that they wouldn't want to let her go. A few people had stood up, citing a moral obligation for the city to return to Pegasus but their voices were drowned out by the majority. The I.O.A. had seen the threat of the Wraith first hand and they preferred having Atlantis protecting the planet directly rather than a galaxy away, especially as the Wraith were not Earth's only enemies. The Goa'uld and the Ori were no longer a threat but others had stepped into the vacuum created by their defeat. The largest problem currently was the ever-expanding Lucian Alliance.

Those same I.O.A. members argued that Carson and Keller had enough Wraith tissue samples here on Earth to continue their work on putting an end to the threat of the Wraith once and for all. Atlantis did not need to return to gather more samples, and as the city had lain beneath the Lantean ocean for ten thousand years, no one could make a strong enough case for why Pegasus could not do without her now.

"These talks have not gone in our favor," Teyla stated solemnly, daring John to contradict her.

John winced and licked his lower lip in an annoying, nervous habit that he had not yet managed to eradicate, wondering when he had become so transparent, but Teyla had a gift for reading between the lines. It had made her an exceptional diplomat and an excellent leader of the Athosians. He knew that for every time they had experienced a problem off-world, there were ten other times when Teyla's negotiating skills and diplomacy had seen them walk away without bloodshed, and often with a good trade and new allies.

"Not exactly," John admitted, and Rodney's fallen expression of dismay merely confirmed that for her.

"Short of stealing Atlantis and flying her back ourselves, there's not a lot more we can do," Rodney fumed, arms crossed over his chest in annoyance.

Ronon growled low in anger, "So, once again, the Lanteans will abandoned Pegasus to its fate."

John tightened his lips and remained silent even though he agreed with Ronon. He was angry on Teyla and Ronon's behalf; angry for all the people in Pegasus who had looked to them in hope of a better future now they no longer had the scourge of the Wraith hanging over them like a dark shadow. He knew Teyla feared that the Genii or another people would form the equivalent of the Lucian Alliance and take over the galaxy. She saw Atlantis as a focal point for bringing order, wealth and prosperity back to all.

However, John could also see the reasoning behind the I.O.A's decision. Michael's reign of terror had come to an end but the legacy left behind was one of starving Wraith afraid to take the risk of culling a potentially infected population in Pegasus, and looking to the Milky Way as a new food source. They had found Earth once, and John knew it was only a matter of time before they found her again. Yet this was exactly why he believed they needed to stay in Pegasus despite the obvious advantages of having Atlantis on Earth as its protector. They needed to keep a close watch on the Wraith as a listening post, and Atlantis was the only Stargate that could dial Earth from Pegasus, providing an early warning system. If the I.O.A. waited for the Wraith to find their way to Earth before attacking, then it would be too late for all of them, as next time it might not be just one ship but a whole armada.

"I tried to explain that even the Ancients knew Atlantis could not save them when they went up against so many Wraith."

The Ancients had won every battle but they had eventually lost the war due to overwhelming numbers. The Wraith had laid siege to Atlantis for a hundred years before the Ancients had sunk the city and escaped back to Earth, locking the Stargate behind them. Earth wouldn't last as long, and the only alternative - releasing Michael's version of the Hoffan plague to poison the Wraith's food source - would see billions of humans die in the Milky Way even with the increased odds on survival from Carson and Keller's work.

John sighed. "At least O'Neill agrees with us. He's argued for Atlantis to return to Pegasus, for tactical as well as scientific and cultural reasons. As have Sam Carter, Daniel Jackson and Woolsey, but the bureaucrats have made up their minds. They want Atlantis to stay on Earth for the foreseeable future."

"I suspected as much for the I.O.A. have offered to transport us to the first Stargate in Pegasus," Teyla stated quietly, though John wondered if it was pressure from O'Neill that had put that offer on the table as it would be prohibitively expensive sending the _Daedalus_ or _Apollo_ that far just to drop off two people. 

She looked to Ronon. "We did not wish to tell you this way for we had considered not accepting their offer, believing Atlantis would be returning to Pegasus shortly. However, perhaps we should take advantage of this generous offer while it is available to us." She sighed. "It is not that I do not wish to fight for the city but I have been away from my people for too long already."

John felt his heart sink at the news, and Rodney looked equally unhappy, aware that Teyla and Ronon's window of opportunity was likely small and closing fast. John knew neither had much of a choice now but to accept or risk permanent exile in the Milky Way. Kanaan and Torren were on New Athos, and John could easily imagine how much Teyla missed her family and her people for he missed them too. Ronon simply wanted to kill Wraith, having vowed to continue the fight until his dying breath, but he didn't want to wait for the Wraith to find their way back to Earth perhaps years in the future.

"I'm sorry," John whispered hoarsely, wishing he could overturn the I.O.A's decision.

It reminded him of another time when the new Lanteans had been forced to return to Earth, though that time without Atlantis. At least the city had stayed in Pegasus, and there was always a chance that Captain Helia and her crew would continue the fight against the Wraith. In the end their arrogance had seen them destroyed by ' _machines_ ' of their own creation - the Asurans - and the new Lanteans had re-taken the city. He knew that this had given hope to many in Pegasus despite the few - like the Genii - who had wanted Atlantis for themselves.

Teyla nodded, understanding. "It is midday. We should take a break." She called to Martinis over the radio, drawing the scientist away from her work and leading her towards the high glass windows overlooking the city.

Turning his back on the beautiful vista of soaring spires, John walked away in the opposite direction, leaving Rodney and Ronon beside the single bench seat. He moved back into the other room and sank down against the wall, pulling a wrapped sandwich out of his pack and dropping it to the floor beside him. He let his gaze fall upon the patterns of orange and gold cast on the cool marble floor from the Californian sunlight pouring through the Ancient stained-glass windows, and sighed heavily. Letting his head hang low for a moment the sound of approaching footsteps brought his head back up, but John didn't need to glance around to know it was Rodney.

"John?"

Licking his lips, John pondered over what he could say, startling when Rodney huffed loudly before dropping down beside him. John barely had time to move his turkey sandwich out of harm's way, sending an irritated glance towards Rodney but Rodney simply waved off John's annoyance with an eye roll.

"Please... I'd be doing both you _and_ me a favor by squashing it."

Deciding not to get back into another argument over his decision to go with the lemon-mayo dressing, John ignored the jibe and changed the subject.

"Atlantis should be going back to Pegasus with them. _We_ should be going back with them," John stressed, meaning him and Rodney, because Teyla and Ronon were more than team; they were family.

"Yes... but we're not, and sitting here moping about it isn't going to change that."

"I'm not moping," John exclaimed, smacking Rodney on the arm with the back of his hand.

He was irked because it was exactly what he was doing. Moping. He had spent every waking moment of this past week trying to persuade the I.O.A. to change its decision and allow Atlantis go home. He knew others had been just as vocal, especially Rodney, but the I.O.A. had insisted that Atlantis _was_ home, so it had all been for nothing so far. 

"Eventually they'll come to their senses... plus I have a few ideas."

"Rodney," John warned, low and hard. Rodney might be one of the smartest people in two galaxies but he could still be one of the most stupid on occasion too, especially when his heart was involved.

"Don't worry, Sheppard. I'm not planning to do anything without talking to you first."

Feeling slightly relieved, John unwrapped his sandwich, and they both ate in companionable silence.

***

Tensions between the various countries comprising the I.O.A. increased over the next week as each tried to dictate who should hold more control over the city and any Ancient technology discovered. They argued that the Americans already had Earth's Stargate buried deep within their borders, refusing access unless it went through official Homeworld channels, and that the Americans had locked down access to the Antarctic Ancient outpost even though that was supposedly on neutral territory.

John tried to stay clear of all these arguments but as the commanding officer of the military - and an American - he was drawn into them both officially and unofficially. He watched as Rodney slumped into the seat opposite him in the Mess Hall, looking frazzled and irritated. Rodney barely grunted a greeting before attacking his meal as if it might disappear from his tray at any second. Admittedly that had happened occasionally, but Ronon was no longer on Atlantis having left on the _Daedalus_ with Teyla two days earlier, and John had already had his fill of canteen food. He smiled wryly, picking at the fruit cup he'd chosen for dessert, and waited for Rodney to start ranting over whatever had got him all annoyed.

"This is your fault," Rodney stated suddenly, jabbing his fork in John's direction.

John pulled back a fraction in surprise, wondering why Rodney was blaming him for whatever had crawled up his ass.

"My fault?"

"Yes! No! I mean your idiotic government that thinks everything should be stamped with the Stars and Stripes." He glared at John. "How many times must I tell all those imbeciles at the I.O.A. that I'm Canadian?"

"Well you could try being a little nicer," John teased, knowing how much the Canadian stereotype riled Rodney. Sure enough, Rodney snarled at him and John laughed.

Rodney rolled his eyes but at least he was starting to see the funny side. John saw him glance around to check that no one was listening in before leaning in towards John, his voice lowered.

"I wouldn't mind so much if this wasn't all part of the plan."

"The plan?" John asked, keeping his voice low too.

"Yes. The Plan! The plan to force the I.O.A. to let Atlantis head back to Pegasus."

"There's a plan?"

"I told you-."

"No you didn't-."

"Huh! Really? I thought you knew all about Plan Babel."

John mouthed the words ' _Plan Babel_ ' with a frown. "No, I don't."

Rodney looked around again. "We've been stirring up a little international unrest. Each country wants Atlantis floating within their international waters so we've come up with obviously flimsy excuses for why it has to remain in U.S. waters. Really flimsy."

"That's a terrible plan. Wars have started over less... and we kind of need the I.O.A." John frowned. "Did Teyla agree to this?" The heat rising in Rodney's cheeks gave him his answer because Teyla would never agree to a plan that could cause a war to break out on Earth, not even to get Atlantis back in Pegasus. "You have got to stop Plan Babel right now," John insisted quietly.

"It's the only way-." Rodney argued back but John cut him off.

"Find another."

Rodney grumbled under his breath but John leaned back, confident that Rodney would see sense and figure out a new plan. He knew this was likely just a backlash of having to say goodbye to Teyla and Ronon. For all the insults flying back and forth, including the Conan and Xena references that Teyla had made Rodney pay for with a few bruises from her Bantos rods, they were family. John hated knowing he was not going to be there to protect their backs if they had to go up against the Wraith or another group like the Genii.

"So... Iron Man or Captain America?"

"Oh please! Iron Man."

He distracted Rodney with his views on the latest Avengers movie, enjoying the mocking as Rodney started on a far different and healthier rant.

***

When he next saw Rodney, John knew instantly that something was wrong. 

They had taken to sitting out on the West pier on calm evenings, with the lights of Atlantis glowing behind them in what many of the latest crop of scientists and military described as the new Tenth Wonder of the World. Admittedly, Atlantis was beautiful, and John could think of nowhere more magical.

Unfortunately, with so many new people in the city, the walkway along the pier was no longer as private as it had once been. John gave a tight nod to an unfamiliar couple out walking hand-in-hand, but fortunately they were too wrapped up in the romance and beauty of the city, and kept on walking after the greeting rather than stopping to try to engage him in conversation.

Rodney arrived a few minutes later, looking bow-shouldered and miserable. He sat down beside John, letting his feet hang over the edge and murmured a soft thanks as John pressed a cold beer into his hand.

"Hard day at the office, dear?" John joked.

When Rodney remained silent, John's fears grew until he couldn't remain quiet any longer.

"What's going on, Rodney?" he asked softly.

Rodney shook his head, and all the warning bells went off in John's head because Rodney was never quiet unless it was serious.

"Rodney?" he drew out Rodney's name in friendly warning, aware of the impact on his best friend when he used that no-nonsense tone. It had the desired effect, and Rodney sighed heavily and half-turned towards him.

"Jennifer is stepping down as CMO of Atlantis. She wants more time for her research." He paused a moment. "They're going to offer the post back to Carson."

"Okay. That's not so bad."

John liked Carson. He seemed to have better instincts than Keller, and he had the ATA gene. Atlantis liked him better, and now he'd gotten over the worst of his fear regarding Ancient technology, he was able to do things on Atlantis that were far beyond Keller's abilities. Not that it was Keller's fault. Like Radek, she was one of the 48% who had not reacted positively to the gene therapy.

It really wasn't so bad overall, which was why John's internal warning sixth sense was still vibrating because he suspected there was worse to come. "What else?"

Rodney gave him a dismayed look. "Jennifer... wants to work on Earth."

John felt something in his chest twist, seizing his breath for a moment as he wondered if this was Rodney's way of telling him that he would not be staying on Atlantis if they did convince the I.O.A. to let her return to Pegasus. It had always been a possibility, lying like a dark shadow cast around his heart. He took a swallow of his beer and waited for the fatal blow to land, almost choking when Rodney spoke next.

"We had a fight. She wants Atlantis to remain on Earth so she can continue working here, and she wanted me to stop trying to persuade the I.O.A. otherwise." He swallowed. "I-I can't do that." He shrugged. "She... thinks we need to take a break. To _assess our priorities_." His fingers made quotes in the air.

John winced because he'd heard that line before, from Nancy. The break had become permanent and had ended in divorce. Even though it was what they both needed and wanted, and it was amicable, giving up on their marriage had still hurt. Rodney and Jennifer were not married, but John knew he'd been thinking of asking her when the time was right. Except something had been holding Rodney back because if he couldn't find the right time while sitting in relative safety on Earth for the past six weeks, then when would it have been the right time? It looked as if the answer now would be never, and though John had hated the idea of losing Rodney to Keller for selfish reasons, he had wanted Rodney to find happiness, even if that was with Jennifer Keller.

"I'm sorry."

Those two words seemed so inadequate but John couldn't think of anything else he could say without revealing his own feelings for Rodney, and without vilifying Keller. They seemed to be enough though as Rodney gave him a crooked half-smile before accepting another beer off him. John hated talking about feelings and relationships, but he could listen, so he remained silent and waited for Rodney.

"I'm... surprisingly fine about it." Frown lines creased his forehead and he grimaced. "And that's part of the problem." He turned more fully. "Did I tell you she wanted me to meet her father? And did you know she has three cousins who are all doctors too? Medicine not..." He waved a hand at himself. "Can you imagine the family reunion? I feel physically unwell just thinking about it. At least Jeannie is a real doctor."

"I think you'll find they are real doctors too," John murmured, only for Rodney to snort derisively.

"Medicine? It's all chicken bones and rattles."

"Yeah, that comparison would have gone down well at the Keller Family Gathering," John remarked.

"Yes, well, at least I don't have to worry about that anymore."

John chewed on his lower lip and came to a decision. "I promised to spend a few days with my brother... with Dave. Come with me."

Rodney looked right at John, looking a little surprised by the invitation.

"Is that the place with the horses? Ronon mentioned horses. Because I think I might be allergic to horses."

"You going to say yes or not?"

"Yes. Yes I'd... Yes."

"Good."

***

The few days spent with Dave turned out well, all things considered. Rodney had been.... Rodney, but instead of being offended by some of the less than stellar comments, Dave had found it refreshing to be around someone who spoke their mind. One of the reasons why John had never wanted to be a part of the family business was because he had hated all the fake smiles and phony solicitude, and he had hated the pretense and office politics - schmoozing as his father had called it. Dave had excelled at it, like their father, but over those few days John had seen his brother's polite persona thawed by Rodney's brashness and honesty until Dave was reacting just as candid in response.

Watching their friendly bickering over the breakfast table on the last day made John smile, recalling similar moments with Dave when they were growing up together. He could tell by the sparkle in two sets of blue eyes that they were both enjoying the debate, and he shared a soft smile and an eye roll with his sister-in-law.

Grace was a surprise. He had only met her for the first time at his father's funeral, having deliberately cut himself off from the family after the argument and his father's threat to disown him. She was smart and lovely, and far more down to earth than John had expected. He could tell that she loved his brother deeply.

Whenever anyone asked what had caused the rift between him and his dad, John told them they had argued when he enlisted in the Air Force rather than take on the family business. He told them he wanted to fly, but John could have flown company helicopters or the family jet. He'd already gained his light aircraft pilot's license, having taken lessons as soon as he was legally old enough.

The rift between him and his father had come over a man who saw an opportunity to get hold of some of the Sheppard family fortune by threatening to reveal John's bisexuality. At the time John was seeing Nancy and they had just announced their engagement. His father had promised to make the problem go away and the wedding had gone ahead a few months later, though with this shadow of fear hanging over it. Nancy had put it down to pre-marital nerves but John had half-expected Andrew to jump up when the priest asked if there was any reason why he and Nancy should not be lawfully wed.

Nothing had happened though.

Although he hated the idea, John assumed his father had paid off Andrew, but he bumped into a mutual friend a few months later and discovered Andrew had died in a car accident just before the wedding. John managed to get hold of the accident report and although it all looked above board, he could never shake the feeling that his father had arranged for that accident. Patrick Sheppard had been a ruthless businessman and he certainly had the money, position and power to make a problem like Andrew go away permanently.

They had argued over it, and John had walked out after his father threatened to cut him off, joining the Air Force more to spite his father than anything, to prove that he didn't need his father's money. Nancy had left him not long after because she had never signed up to be a military wife, moving from one station to the next and living in a series of bland military accommodation. Then there were the weeks at a time spent alone because he was on exercise, or on tour in a unstable country, or on training courses. John had never held her decision to leave him against her.

Dave cornered him about an hour before he and Rodney were due to head back to Atlantis.

"So, is he the one?"

"The one?" 

Dave had made veiled hints about Ronon at the funeral but John had deliberately chosen to ignore them, but he should have known he couldn't hide forever. Dave had known about John's bisexuality from those summer days in California, when he'd caught John appraising not just the bikini-clad girls but the half-naked guys on the beach too.

"John, it never bothered me when we were teens, and it doesn't bother me now. So?"

John sighed. "I... like him, but he's not inter-."

Dave grinned. "If you weren't so busy trying to keep your eyes off him, you'd notice he spends a lot of time checking you out when he thinks no one is looking."

Not much more was said but Dave had planted a small seed of hope within John that day.

***

It took another two months of arguments flying back and forth before the I.O.A. finally saw sense and agreed to allow Atlantis to return to Pegasus, and it was only then in the understanding that should Earth need her, Atlantis would come to her aid. Of course it helped that Rodney had spent those months perfecting his calculations for the Wormhole Drive, which meant near instantaneous travel between the two galaxies, like using a Stargate.

"I handed over the equations as a goodwill gesture," Rodney stated smugly. "That should also provide a means for Earth to rescue the crew of _Destiny_ without resorting to hijacking any more Stargates on naquadria-rich planets like Langara," he added airily.

John was still pretty pissed about that mission because it had been poorly thought out, and had gone south fast, putting Rodney's life in danger. He was just glad the Langarans had ordered the Stargate shut down before the wormhole engaged for, according to Rodney, they were pissed enough to consider throwing the lot of them, including Rodney and Woolsey, through the gate onto _Destiny_. It was also fortunate that the Langarans were willing to negotiate for a release of the hostages as John didn't think he would get away with another black mark on his permanent record from storming Langara to free Rodney.

"I hope that's not the same drive some alternate version of you put on the _Daedalus_ , because that didn't go so well."

Predictably, Rodney rolled his eyes. "Ha, ha, Sheppard."

John grinned and saw Rodney glance away shyly, something he had been doing a lot over the past few weeks. Rodney was brash and loud about his intelligence and his work, and how important both were for the future of two galaxies. The only times John had seen Rodney acting less than confident was when he was dealing with personal issues, especially people he cared about. On a professional level, he could rant better than anyone, with words falling as sharp as razor blades, clean and quick as they drew blood. On a personal level, he was reduced to a blathering idiot, shy and uncertain, with words failing him as he, unintentionally, insulted rather than complimented the person he was trying to impress.

More and more frequently over the past weeks Rodney had become that blathering idiot around John - stumbling over his words in more intimate situations. Things they had done together a thousand times now had Rodney wringing his hands nervously and tripping over his own tongue. He'd no longer sit shoulder to shoulder on John's bed watching movies and TV shows, choosing the chair instead, and John missed the warmth of his body next to him.

It gave John hope even as it filled him with dismay because there were two possibilities.

Rodney may have finally realized that John's feelings for him went far beyond the platonic, and that John wanted more than simple friendship with him. So, perhaps the strange behavior was Rodney's way of showing how uncomfortable he was with that knowledge.

Or maybe it was the exact opposite, with Rodney discovering he had a reciprocal crush on John.

John knew which scenario he preferred but without more data to support it, his own social inadequacies got the better of him, leaving him too scared to risk losing even this strained friendship with Rodney. At least Rodney did not seem to be pining over Keller. He had said he was fine with the break up and John knew that could have simply been bravado at the time, but as soon as the announcement went out about Atlantis, Keller requested a transfer to the SGC, and Rodney had not been bothered at all. If anything, he seemed a little relieved that she would not be going back to Pegasus with them.

"So how are the preparations going?" John asked, and he was rewarded by a wide smile.

"Actually, we were ready to take off months ago." He rubbed his hands together briskly. "We're just waiting for the last crates of supplies to be brought on-board. Might as well make good use of the fact that we are sitting less than fifty miles from Radio Shack and Walmart."

John grinned because he'd spent the past few months pushing through the quartermaster's requisitions on behalf of the military and civilians on Atlantis in the hope that Atlantis would return to Pegasus. The ten thousand-year-old beds had lasted remarkably well and were actually quite comfortable, but despite numerous explorations into some of the residential areas of the city, no one had yet to discover a bed that was big enough to accommodate two sleeping adults. The sociologists suspected the Ancients simply did not sleep together. Secretly, John wondered if that was why all the Ancients they had ever met were so uptight and repressed. Most had been seeking Ascension so they had likely been trying to cast off all earthly connections, starting with the intimate-carnal ones.

John's soldiers were in the process of unloading the latest transport from the mainland, which included larger beds with decent mattresses for all expedition members, plus extras for guest accommodations. The quartermaster had taken over a tower that was the size of a small warehouse to store all the rest of the acquisitions including uniforms, clothing, dried foods, lab equipment, trade items, electronics, and enough coffee beans to keep Rodney and his minions caffeinated for a year if the _Daedalus_ stopped its supply runs.

By the time Rodney stumbled back to his quarters in the early hours of the morning, the marines would have set up Rodney's new double-size bed with its special orthopedic mattress. As for John, he was looking forward to having a bed that was both long enough and wide enough to stretch out in, having spent the past few years sleeping in a bed that was intended for either a short Ancient or an adolescent. Rodney had ribbed him over that bed on numerous occasions. Perhaps now he would be able to entice Rodney to sit side-by-side with him on the bed again while they watched movies, and in far more comfort with their backs supported by pillows stacked against the wall and their legs stretched out in front of them.

He smiled as he anticipated Rodney's reaction.

***

"Rodney. Sleep well?" John said in greeting, ducking his head to hide more than just his smile because Rodney looked... amazing. He looked better rested than usual despite the late night, and John hoped that was because of the new bed. Rodney had often complained about how many times he had awoken in the night trying to get comfortable on his narrow bed.

John watched as Rodney sank into the seat opposite him, busying himself for a moment with the items on his breakfast tray before looking up and capturing John's eyes with his own. His head tilted to one side a little as he studied John for a moment before speaking.

"I... spoke to the quartermaster and he said it was your idea."

"My idea?" John feigned ignorance even though he knew exactly what Rodney was talking about.

"Yes. Apparently we have a whole tower full of supplies, and every member of the expedition now has more than just the basic amenities... and new beds." Rodney shook his head, offering an incredulous smile. "I'm... astounded that you managed to convince the I.O.A. and US Government to-."

"I just pushed through the acquisition orders and requests, Rodney. O'Neill rubber-stamped them. No questions asked." 

John didn't mention that O'Neill had even added a few items that would seem extravagant to the normal pen pushers - golf and fishing accessories, baseballs, bats and catcher's mitts, footballs and basketballs, and a whole lot more equipment to outfit a proper gymnasium, as well as real board games. O'Neill had justified the additional expense as looking after the mental and physical health of the expedition, and no one on the I.O.A. or budget committees had argued against him. John suspected that O'Neill had plans to visit Atlantis in Pegasus, perhaps use it as a semi-vacation spot. He had been quite taken with the city when he'd stayed there before at the request of Captain Helia, and Atlantis had liked him too because he had a strong expression of the ATA gene, like John.

John also didn't mention that he had been given permission to approach Sheppard Industries on behalf of the I.O.A. to bring their Research and Development department into the Stargate program. By special request he would be giving Dave the Atlantis tour in a few days time. He licked his lower lip nervously because Dave's arrival had given him a personal deadline to speak to Rodney about... them. He knew Dave would start asking questions as soon as they were alone, and he wanted to show his older brother that he had taken his words to heart and acted on them.

Rodney rolled his eyes gently, smiling softly. "I just wanted to say... _my back_ thanks you." His face turned serious. "John... There's something..." he paused, opening and shutting his mouth twice before starting again. "I need to-."

The clatter of a breakfast tray hitting the floor, followed by laughter, had Rodney looking around the slowly filling Mess Hall.

"Rodney, I have something I need to say to you too. In private. Why don't we meet out on the pier tonight?"

"Yes, yes. Good idea. Tonight. Usual time?"

They turned to official topics as they finished breakfast, then parted to carry out their duties for the day.

As the hour drew closer, John became more nervous. He knew that no matter what happened, things would never be the same between him and Rodney after this evening, but with the lifting of DADT and the restructuring of the off-world teams, he had no reason to deny himself this chance of happiness any longer. He'd known from the early days of the expedition that Rodney was special to him, and the years had merely served to turn desire into love. He wanted Rodney and an offhand comment from Jeannie only yesterday had given him even more hope that Rodney might want that too. It had given him the courage to finally admit those feelings and hopes out loud to Rodney.

With just fifteen minutes to go, John stood in front of his dressing mirror and gave himself a soft pep talk.

"You can do this, John. You've faced down Wraith. You've flown a nuclear bomb into a hive ship. Hell, you've scaled the outside of the central tower to reach Rodney. You **can** do this."

He straightened the collar of his shirt and took a deep breath before snagging the six-pack of beers from the desk on his way out. He found Rodney already waiting for him in the usual spot and sank down next to him, offering him a beer.

"Thanks."

John opened his own beer and took a generous swallow before turning slightly to study Rodney in profile. Rodney was strangely quiet and a little tense, but then he'd implied at breakfast that he had something to say to John too. John was tempted to wait and let Rodney go first but it seemed cowardly on his part. He had practiced what he wanted to say in the mirror earlier, but the words seemed to stick in his throat now that he was sitting next to Rodney. His best friend. It seemed stupid but words had never come easily to him when it mattered on a personal level. He had no problem giving orders or speeches professionally, but matters of the heart scared the life out of him, and he'd always been better at taking action rather than talking anyway.

It occurred to him then that maybe he didn't need to say anything to Rodney. Maybe what he needed to do was show him instead. He emptied his can and set it down, waiting for Rodney to do the same before reaching out and cupping Rodney's face, turning Rodney to face him. He could see the questioning in Rodney's eyes, in the frown creasing his forehead, and in the tilt of his slightly parted lips. Before Rodney could form a single word, John leaned in and pressed his lips to Rodney's in a quick, soft kiss that lasted only seconds. He pulled back to register the stunned look in Rodney's eyes.

"Was that...?"

"A kiss?"

Rodney blinked rapidly. "Does that mean...?"

"That I ... I like you."

"Oh thank God!"

Before John could remind Rodney that he was supposed to be an Atheist he found himself wrapped in those muscular arms and with Rodney's mouth pressed hard against his own, as if trying to suck the very air from his lungs, and John kissed him back just as hard. By the time they parted, both of them were breathing heavily and John stared deep into Rodney's eyes, wishing it wasn't quite so dark on the pier despite the lights illuminating the city behind them. The still tight grip of Rodney's hands on his shoulders and the soft breaths that were close enough to warm his face told him all he needed to know, and he relaxed as Rodney leaned in again, meeting him partway in another softer kiss.

This time when they pulled back, Rodney spoke.

"Is this what you wanted to tell me?"

"Yeah."

"How... How long?"

"A while."

"Months?" Rodney questioned. "Years?" John winced. "Oh my God! Years. You've been pining away for me for years."

Irritated by the smug grin, John smacked Rodney's hand away and started to rise, only to be pulled back down.

"Oh, no, no, no. We haven't finished here yet." Rodney's grip eased and his expression turned both serious and awed. "I-I wanted to meet you out here to tell you that I... liked you too."

"But I said it first," John reminded him, turning that to his advantage as Rodney hated coming in second to anything.

"Actually, you never _said_ anything," Rodney accused in turn, looking up as John gained his feet.

John offered a hand to Rodney, pulling him to his feet.

"I made the first move." He began to steer Rodney back towards the city.

"Technically, I started back at breakfast, and if Doctor Jezebel..."

"Jezebna."

"...hadn't dropped her tray-."

"But she did, and so you missed your chance to be first."

Rodney began to splutter in indignation while John grinned like a small kid handed the best treat ever. He shrugged nonchalantly as Rodney continued a one-sided argument all the way to the transporter. John let his hand hover over the control panel, and sent a heated look towards Rodney. 

"Are we really going to argue over who said it first? Or are we going to prove that actions can be a lot more fun than words?" John asked, and saw Rodney's eyes darken.

"Yes... I mean no. More kissing, less talking is good."

John pressed the area closest to his quarters, and only minutes later the door was locked behind them, and they were stripping and kicking off shoes as John slowly led them to the new, double-sized bed in his quarters. He must have seen Rodney naked a dozen times or more but this time he could look freely. This time he could reach out and touch and hold. He could press kisses against the tilted corner of Rodney's mouth, could splay his fingers over the curve of one rounded ass cheek, and wrap his hand around their hard cocks. This time he could slowly bring them both to climax and swallow Rodney's cries of passion as they shuddered through their climax only minutes apart.

This time he could awaken with the first early rays of the morning sun and see Rodney's face on the pillow next to his, and listen to his soft snores, knowing every morning could start this way in future.

***

When Departure Day arrived, John could feel the excited atmosphere in the city as he sank into the control chair. Rodney was buzzing around from console to console, barking out orders to his scientists but, eventually, he stopped and turned to John. His eyes had never looked so beautiful, sparkling with love and excitement, and his smile was bright and carefree. When he nodded at the same time that John heard Woolsey give the order to take off, John felt Atlantis expand inside his mind in a way never felt before.

Alive and eager to obey his commands.

The city lifted very slowly from the Pacific Ocean and climbed into the blue skies of Earth at the start of her journey home. Moments later she was heading out of the solar system, leaving Earth far behind. John concentrated hard and glanced across the room as soon as the Wormhole Drive engaged successfully, heading for Pegasus. He caught Rodney's eyes, and smiled as he recalled waking up beside Rodney just a few hours earlier, remembering the early morning sunlight slanting through a chink in the curtains. He sighed in memory of the soft kisses that grew more urgent as they moved together, gasping out their release and relaxing back into each other's arms in the afterglow.

In a few more hours they would be settling back down on Lantea.

Atlantis was going home, but John realized that as long as he had Rodney in his life, he was already home.

END

[ ](http://archiveofourown.org/works/550301)

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